Contacts of the helix formed by residues 1058 - 1079 (chain B) in PDB entry 6KJV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR1058 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014B LEU* 4.7 4.9 - - - -
1056B VAL* 5.7 3.1 - - + +
1057B ILE* 1.3 81.4 - - - +
1059B LYS* 1.3 65.9 + - - +
1060B ASP* 4.0 4.0 + - - +
1061B GLU* 3.2 32.6 + - - +
1062B ALA* 3.2 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1059 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B LEU* 4.7 26.5 - - + -
1014B LEU* 4.9 7.3 - - + +
1058B THR* 1.3 76.0 - - - +
1060B ASP* 1.3 64.2 + - - +
1062B ALA* 3.2 9.0 + - + +
1063B GLU* 2.9 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1060 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058B THR* 3.3 5.1 + - - +
1059B LYS* 1.3 83.0 + - - +
1061B GLU* 1.3 61.2 + - + +
1063B GLU* 3.2 9.8 + - - +
1064B LYS* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1061 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049B ILE* 3.7 30.0 - - + +
1051B ARG* 5.7 5.2 - - - +
1056B VAL 5.0 0.7 - - - +
1057B ILE* 3.6 35.7 - - + +
1058B THR* 3.2 25.2 + - - +
1059B LYS 3.4 0.2 - - - -
1060B ASP* 1.3 77.4 - - + +
1062B ALA* 1.3 57.8 + - - +
1064B LYS* 3.3 17.4 + - - +
1065B LEU* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1062 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B LEU* 4.1 15.5 - - + -
1013B ARG 5.2 1.1 - - - +
1027B GLY* 4.1 14.1 - - - -
1028B ILE* 3.5 21.0 + - + +
1057B ILE* 3.9 9.1 - - + +
1058B THR 3.2 13.4 + - - +
1059B LYS* 3.4 10.1 - - - +
1061B GLU* 1.3 78.5 - - - +
1063B GLU* 1.3 57.0 + - - +
1065B LEU* 3.4 6.6 + - - +
1066B PHE* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1063 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028B ILE* 4.6 10.6 - - + +
1059B LYS* 2.9 42.1 + - + +
1060B ASP* 3.2 12.8 + - - +
1062B ALA* 1.3 76.9 - - - +
1064B LYS* 1.3 63.6 + - - +
1066B PHE* 3.2 23.3 + - - +
1067B ASN* 3.0 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1064 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049B ILE* 5.8 7.2 - - + +
1060B ASP* 2.9 17.4 + - - +
1061B GLU* 3.4 19.1 - - - +
1062B ALA 3.3 0.2 - - - -
1063B GLU* 1.3 76.1 - - - +
1065B LEU* 1.3 62.1 + - - +
1067B ASN* 3.2 9.2 + - - +
1068B GLN* 3.1 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1065 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030B HIS* 4.7 22.0 - - + +
1048B ALA 5.8 2.7 - - - +
1049B ILE* 5.5 7.0 - - + -
1061B GLU 3.0 16.9 + - - +
1062B ALA* 3.8 6.7 - - - +
1064B LYS* 1.3 76.0 - - - +
1066B PHE* 1.3 56.5 + - - +
1068B GLN* 3.2 18.7 + - - +
1069B ASP* 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1066 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003B PHE* 3.5 56.1 - + + -
1006B LEU* 3.6 23.8 - - + -
1007B ARG* 5.0 2.9 - - + -
1028B ILE* 3.5 49.6 - - + +
1062B ALA 2.9 17.4 + - - +
1063B GLU* 3.4 22.4 - - - +
1064B LYS 3.2 0.2 - - - -
1065B LEU* 1.3 74.1 - - - +
1067B ASN* 1.3 65.8 + - - +
1069B ASP* 3.2 6.3 + - - +
1070B VAL* 3.0 44.7 + - + +
1103B PHE* 4.1 8.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1067 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003B PHE* 4.1 32.3 - - - -
1063B GLU* 3.0 28.1 + - - +
1064B LYS* 3.5 9.9 - - - +
1066B PHE* 1.3 75.0 - - - +
1068B GLN* 1.3 63.9 + - + +
1070B VAL* 3.3 1.2 + - - +
1071B ASP* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1068 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030B HIS* 5.4 4.5 - - - -
1048B ALA* 4.6 13.4 + - - +
1064B LYS* 3.1 33.0 + - + +
1065B LEU* 3.2 17.7 + - - +
1067B ASN* 1.3 78.2 - - + +
1069B ASP* 1.3 65.6 + - - +
1071B ASP* 3.4 4.8 + - - +
1072B ALA* 3.0 23.6 + - - +
1075B ARG* 4.5 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1069 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028B ILE 4.2 5.0 - - - +
1030B HIS* 2.8 51.8 + - - +
1065B LEU 2.9 22.8 + - - +
1066B PHE* 3.2 6.6 + - - +
1068B GLN* 1.3 78.7 - - - +
1070B VAL* 1.3 58.8 + - - +
1072B ALA* 3.3 7.8 + - - +
1073B ALA* 3.0 27.0 + - - +
1103B PHE* 3.5 25.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1070 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002B ILE* 4.5 19.5 - - + -
1003B PHE* 3.9 33.9 - - + -
1006B LEU* 4.0 15.5 - - + -
1066B PHE* 3.0 39.9 + - + +
1067B ASN 4.0 1.1 - - - +
1069B ASP* 1.3 76.3 - - - +
1071B ASP* 1.3 63.7 + - - +
1073B ALA* 3.1 7.4 + - - +
1074B VAL* 3.1 28.3 + - + +
1099B ILE* 4.9 7.6 - - + -
1103B PHE* 4.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1071 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067B ASN 3.0 17.0 + - - +
1068B GLN* 3.8 4.5 - - - +
1070B VAL* 1.3 78.0 - - - +
1072B ALA* 1.3 61.9 + - - +
1074B VAL* 3.1 13.3 - - + +
1075B ARG* 3.0 49.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1072 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068B GLN 3.0 14.4 + - - +
1069B ASP* 3.5 11.0 - - - +
1070B VAL 3.2 0.2 - - - -
1071B ASP* 1.3 75.8 - - - +
1073B ALA* 1.3 58.9 + - - +
1075B ARG* 3.3 18.1 + - - +
1076B GLY* 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1073 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069B ASP 3.0 13.4 + - - +
1070B VAL* 3.1 10.9 + - - +
1072B ALA* 1.3 75.5 - - - +
1074B VAL* 1.3 64.4 + - - +
1076B GLY* 3.1 3.2 + - - -
1077B ILE* 3.0 26.9 + - - +
1099B ILE* 4.0 21.3 - - + +
1102B VAL* 4.2 20.8 - - + +
1103B PHE* 4.6 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1074 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070B VAL* 3.1 17.1 + - + +
1071B ASP* 3.1 21.8 - - + +
1073B ALA* 1.3 77.4 - - - +
1075B ARG* 1.3 65.2 + - + +
1077B ILE* 3.2 8.6 + - - +
1078B LEU* 3.0 36.8 + - + +
1087B TYR* 4.4 12.3 - - + +
1099B ILE* 3.7 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1075 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068B GLN* 4.5 2.8 + - - +
1071B ASP* 3.0 35.4 + - - +
1072B ALA* 3.6 27.9 - - - +
1074B VAL* 1.3 81.4 - - + +
1076B GLY* 1.3 63.3 + - - +
1078B LEU* 3.9 8.4 - - + +
1079B ARG* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1076 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072B ALA 2.9 14.9 + - - -
1073B ALA* 3.1 4.5 + - - -
1075B ARG* 1.3 77.6 - - - +
1077B ILE* 1.3 61.5 + - - +
1079B ARG* 3.1 14.8 + - - +
1080B ASN* 3.3 14.4 + - - +
1102B VAL* 5.9 0.2 - - - -
1107B GLU* 4.5 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1077 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073B ALA 3.0 16.3 + - - +
1074B VAL* 3.2 7.8 + - - +
1076B GLY* 1.3 75.0 - - - +
1078B LEU* 1.3 63.6 + - + +
1080B ASN* 3.1 22.1 + - - +
1083B LEU* 3.8 22.9 - - + +
1084B LYS* 3.6 5.6 + - - +
1087B TYR* 3.7 40.4 - - + -
1098B LEU* 4.4 6.5 - - + +
1099B ILE* 3.9 35.9 - - + +
1102B VAL* 3.6 32.5 - - + -
1107B GLU* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1078 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074B VAL* 3.0 29.9 + - + +
1075B ARG* 3.9 8.1 - - + +
1077B ILE* 1.3 76.4 - - + +
1079B ARG* 1.3 56.1 + - - +
1080B ASN 3.3 1.6 + - - +
1084B LYS* 3.7 34.0 - - + +
1087B TYR* 4.0 32.8 - - + -
1088B ASP* 4.0 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1079 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075B ARG 3.1 18.4 + - - +
1076B GLY* 3.1 6.5 + - - +
1077B ILE 3.1 1.0 - - - -
1078B LEU* 1.3 77.3 - - - +
1080B ASN* 1.3 59.2 + - - +
1081B ALA 4.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il